Added the kmer filter to LCS alignments, and now obiblobs containing

encoded sequences are directly put in int16_t arrays for the alignment

src/upperband.h

@@ -0,0 +1,26 @@
+
+#ifndef UPPERBAND_H_
+#define UPPERBAND_H_
+
+// TODO doc
+
+#include <stdbool.h>
+#include <stdio.h>
+
+#include "obiblob.h"
+#include "obiview.h"
+#include "obidmscolumn.h"
+
+
+typedef struct {
+	unsigned char* table;      	// 4mer occurrence table built using the build_table function
+	int32_t        over;        // count of 4mers with an occurrence greater than 255 (overflow)
+} Kmer_table_t, *Kmer_table_p;
+
+
+Kmer_table_p hash_seq_column(Obiview_p view, OBIDMS_column_p seq_col);
+void align_filters(Kmer_table_p ktable, Obi_blob_p seq1, Obi_blob_p seq2, index_t idx1, index_t idx2, double threshold, bool normalize, int reference, bool similarity_mode, double* score, int* LCSmin);
+void free_kmer_tables(Kmer_table_p ktable, size_t count);
+
+#endif
+